diff --git a/nipype/interfaces/io.py b/nipype/interfaces/io.py
index e11ba47479..c72aab4a34 100644
--- a/nipype/interfaces/io.py
+++ b/nipype/interfaces/io.py
@@ -28,6 +28,7 @@
 import tempfile
 from os.path import join, dirname
 from warnings import warn
+from packaging import version
 
 from .. import config, logging
 from ..utils.filemanip import (
@@ -2733,6 +2734,10 @@ class BIDSDataGrabberInputSpec(DynamicTraitedSpec):
     return_type = traits.Enum('file', 'namedtuple', usedefault=True)
     strict = traits.Bool(desc='Return only BIDS "proper" files (e.g., '
                               'ignore derivatives/, sourcedata/, etc.)')
+    domains = traits.Either(None, traits.List(),
+                            usedefault=True,
+                            desc='(Optional): Pass list of domains '
+                            '(e.g. ["bids", "derivatives"]) for file searching.')
 
 
 class BIDSDataGrabber(LibraryBaseInterface, IOBase):
@@ -2808,14 +2813,31 @@ def __init__(self, infields=None, **kwargs):
 
     def _list_outputs(self):
         # Version resilience
+        import bids
+        from packaging import version
         try:
             from bids import BIDSLayout
         except ImportError:
             from bids.grabbids import BIDSLayout
+
+        pybids_ver = version.parse(bids.__version__)
         exclude = None
         if self.inputs.strict:
             exclude = ['derivatives/', 'code/', 'sourcedata/']
-        layout = BIDSLayout(self.inputs.base_dir, exclude=exclude)
+
+        if pybids_ver < version.parse('0.5'):
+            raise ImportError("pybids must be >= 0.5, "
+            "installed version: {ver}".format(ver=pybids_ver))
+        elif pybids_ver >= version.parse('0.5') and pybids_ver < version.parse('0.6'):
+            layout = BIDSLayout(self.inputs.base_dir,
+                                config=self.inputs.domains,
+                                exclude=exclude)
+        else:
+            # pybids >= 0.6.0
+            if self.inputs.domains is None:
+                self.inputs.domains = ['bids']
+            layout = BIDSLayout((self.inputs.base_dir, self.inputs.domains),
+                                exclude=exclude)
 
         # If infield is not given nm input value, silently ignore
         filters = {}
diff --git a/nipype/interfaces/tests/test_auto_BIDSDataGrabber.py b/nipype/interfaces/tests/test_auto_BIDSDataGrabber.py
index 8acdcc9787..99a81f675a 100644
--- a/nipype/interfaces/tests/test_auto_BIDSDataGrabber.py
+++ b/nipype/interfaces/tests/test_auto_BIDSDataGrabber.py
@@ -6,6 +6,7 @@
 def test_BIDSDataGrabber_inputs():
     input_map = dict(
         base_dir=dict(mandatory=True, ),
+        domains=dict(usedefault=True, ),
         output_query=dict(),
         raise_on_empty=dict(usedefault=True, ),
         return_type=dict(usedefault=True, ),